Utility of North Atlantic Right Whale Museum Specimens for Assessing Changes in Genetic Diversity

Abstract: We examined six historical specimens of the endangered North Atlantic right whale ( Eubalaena glacialis ) using DNA isolated from documented baleen plates from the late nineteenth and early twentieth centuries. Sequences from the mitochondrial DNA (mtDNA) control region from these samples were compared with those from a near-exhaustive survey (269 of approximately 320 individuals) of the remaining right whales in the western North Atlantic Ocean. Our results suggest that there has been only relatively modest change in maternal lineage diversity over the past century in the North Atlantic right whale population. Any significant reduction in genetic variation in the species most likely occurred prior to the late nineteenth century. One historical specimen was from the last documented female capable of propagating one of the maternal lineages in the population today; no females in the existing population have been found to carry this mtDNA haplotype. Analysis of the only specimens from the eastern North Atlantic right whale population ever to be examined revealed that eastern and western North Atlantic right whales may not have been genetically differentiated populations. Loss of gene diversity experienced by North Atlantic right whales over the last century has been modest, and the six decades of protection have been successful in maintaining much of the maternal lineage diversity that was present in the late nineteenth century.     

Changes in microbial community characteristics and soil organic matter with nitrogen additions in two tropical forests

Microbial communities and their associated enzyme activities affect the amount and chemical quality of carbon (C) in soils. Increasing nitrogen (N) deposition, particularly in N-rich tropical forests, is likely to change the composition and behavior of microbial communities and feed back on ecosystem structure and function. This study presents a novel assessment of mechanistic links between microbial responses to N deposition and shifts in soil organic matter (SOM) quality and quantity. We used phospholipid fatty acid (PLFA) analysis and microbial enzyme assays in soils to assess microbial community responses to long-term N additions in two distinct tropical rain forests. We used soil density fractionation and 13C nuclear magnetic resonance (NMR) spectroscopy to measure related changes in SOM pool sizes and chemical quality. Microbial biomass increased in response to N fertilization in both tropical forests and corresponded to declines in pools of low-density SOM. The chemical quality of this soil C pool reflected ecosystem-specific changes in microbial community composition. In the lower-elevation forest, there was an increase in gram-negative bacteria PLFA biomass, and there were significant losses of labile C chemical groups (O-alkyls). In contrast, the upper-elevation tropical forest had an increase in fungal PLFAs with N additions and declines in C groups associated with increased soil C storage (alkyls). The dynamics of microbial enzymatic activities with N addition provided a functional link between changes in microbial community structure and SOM chemistry. Ecosystem-specific changes in microbial community composition are likely to have far-reaching effects on soil carbon storage and cycling. This study indicates that microbial communities in N-rich tropical forests can be sensitive to added N, but we can expect significant variability in how ecosystem structure and function respond to N deposition among tropical forest types.     

Assessing the extinction risk of insular,understudied marine species

Hydrothermal vents are rare deep-sea oases that house faunal assemblages with a similar density of life as coral reefs. Only approximately 600 of these hotspots are known worldwide, most only one-third of a football field in size. With advancing development of the deep-sea mining industry, there is an urgent need to protect these unique, insular ecosystems and their specialist endemic faunas. We applied the IUCN (International Union for the Conservation of Nature) Red List criteria to assess the extinction risk of vent-endemic molluscs with varying exposure to potential deep-sea mining. We assessed 31 species from three key areas under different regulatory frameworks in the Indian, West Pacific, and Southern Oceans. Three vent mollusc species were also examined as case studies of different threat contexts (protected or not from potential mining) to explore the interaction of local regulatory frameworks and IUCN Red List category assignment. We found that these assessments were robust even when there was some uncertainty in the total range of individual species, allowing assessment of species that have only recently been named and described. For vent-endemic species, regulatory changes to area-based management can have a greater impact on IUCN Red List assessment outcomes than incorporating additional data about species distributions. Our approach revealed the most useful IUCN Red List criteria for vent-endemic species: criteria B and D2. This approach, combining regulatory framework and distribution, has the potential to rapidly gauge assessment outcomes for species in insular systems worldwide.     

Importance of Sediment–Water Interactions in Coeur d’Alene Lake,Idaho, USA: Management Implications

A field study at Coeur dAlene Lake, Idaho, USA, was conducted between October 1998 and August 2001 to examine the potential importance of sediment–water interactions on contaminant transport and to provide the first direct measurements of the benthic flux of dissolved solutes of environmental concern in this lake. Because of potential ecological effects, dissolved zinc and orthophosphate were the solutes of primary interest. Results from deployments of an in situ flux chamber indicated that benthic fluxes of dissolved Zn and orthophosphate were comparable in magnitude to riverine inputs. Tracer analyses and benthic-community metrics provided evidence that solute benthic flux were diffusion-controlled at the flux-chamber deployment sites. That is, effects of biomixing (or bioturbation) and ground-water interactions did not strongly influence benthic flux. Remediation efforts in the river might not produce desired water-quality effects in the lake because imposed shifts in concentration gradients near the sediment–water interface would generate a benthic feedback response. Therefore, development of water-quality models to justify remediation strategies requires consideration of contaminant flux between the water column and underlying sediment in basins that have been affected by long-term (decadal) anthropogenic activities.     

Efficacy of extracting indices from large‐scale acoustic recordings to monitor biodiversity

Passive acoustic monitoring could be a powerful way to assess biodiversity across large spatial and temporal scales. However, extracting meaningful information from recordings can be prohibitively time consuming. Acoustic indices (i.e., a mathematical summary of acoustic energy) offer a relatively rapid method for processing acoustic data and are increasingly used to characterize biological communities. We examined the relationship between acoustic indices and the diversity and abundance of biological sounds in recordings. We reviewed the acoustic‐index literature and found that over 60 indices have been applied to a range of objectives with varying success. We used 36 of the most indicative indices to develop a predictive model of the diversity of animal sounds in recordings. Acoustic data were collected at 43 sites in temperate terrestrial and tropical marine habitats across the continental United States. For terrestrial recordings, random‐forest models with a suite of acoustic indices as covariates predicted Shannon diversity, richness, and total number of biological sounds with high accuracy (R² ≥ 0.94, mean squared error [MSE] ≤170.2). Among the indices assessed, roughness, acoustic activity, and acoustic richness contributed most to the predictive ability of models. Performance of index models was negatively affected by insect, weather, and anthropogenic sounds. For marine recordings, random‐forest models poorly predicted Shannon diversity, richness, and total number of biological sounds (R² ≤ 0.40, MSE ≥ 195). Our results suggest that using a combination of relevant acoustic indices in a flexible model can accurately predict the diversity of biological sounds in temperate terrestrial acoustic recordings. Thus, acoustic approaches could be an important contribution to biodiversity monitoring in some habitats.     

Avian Communities of Fragmented South-Temperate Rainforests in Chile

The diversity and relative abundance of south-temperate rainforest birds decreased as the size of the habitat patch decreased. Ecological categories, including endemics, mutualists (pollinators, seed dispersers), understory species, and species dependent on large trees, were not differentially sensitive to patch size. Nevertheless, most of the species with at least marginally significant declines were endemic (6 of 7 species), covered nesters (6 of 7 species), and understory dwellers (5 of 7 species). Some mutualists and big-tree users were also affected. The losses will become more severe as clearing of the forest continues. Possible mitigation measures include leaving small stands of forest and corridors between habitat patches and, in certain circumstances, alternative agricultural practices.     

Multiple paternity and female sperm usage along egg-case strings of the knobbed whelk, <Emphasis Type="Italic">Busycon carica</Emphasis> (Mollusca; Melongenidae)

We used genotypic data from three highly polymorphic microsatellite loci (two autosomal and one sex-linked) to examine micro-spatial and temporal arrangements of genetic paternity for more than 1,500 embryos housed along 12 egg-case strings of the knobbed whelk, Busycon carica. Multiple paternity proved to be the norm in these single-dam families, with genetic contributions of several sires (at least 3.5 on average) being represented among embryos within individual egg capsules as well as along the string. Two strings were studied in much greater detail; five and seven fathers were identified, none of which was among the several males found in consort with the female at her time of egg-laying. Each deduced sire had fathered roughly constant proportions of embryos along most of the string, but those proportions differed consistently among fathers. A few significant paternity shifts at specifiable positions along an egg-case string were also observed. Although the precise physical mechanisms inside a female whelk’s reproductive tract remain unknown, our genetic findings indicate that successive fertilization events (and/or depositions of zygotes into egg capsules) normally occur as near-random draws from a well-but-not-perfectly blended pool of gametes (or zygotes) stemming from stored ejaculates, perhaps in different titers, of a dam’s several mates.     

Development of food preferences: social learning by Belding's ground squirrels Spermophilus beldingi

Summary The mechanisms by which food selection behavior develops may constrain the evolution of optimal foraging, yet these mechanisms have received relatively little attention in recent optimal foraging studies. We used cafeteria-style feeding trials to examine the role of social learning in the development of food preferences by a generalist mammalian herbivore, Spermophilus beldingi. Naive young spent relatively little time feeding and showed no preferences among five plant species offered in their feeding trials. This random pattern persisted for one set of young during two subsequent trials in the absence of their mother. A second group of young squirrels was tested initially alone, once with their mothers, and then once more alone. These squirrels fed more than those in the control group during their final trials, and showed significant preferences among plant species. These paralleled the preferences of their mothers. These results suggest that social learning may be important in the development of feeding behavior in ground squirrels, and provide a possible mechanism for cultural differences in food preferences among populations.     

Genetic evidence of multiple parentage in broods of cliff swallows

Summary Parental exclusion analyses based on allozyme data were performed on 105 families of cliff swallows (Hirundo pyrrhonota) from southwestern Nebraska, USA. The protein products of seve polymorphic loci were resolved from blood, and at least one parental exclusion occurred at six of these loci. One or both putative parents were excluded for 35 nestlings from 22 different families. The mean number of non-kin nestlings in these families was 1.59. Non-kin nestlings were found in families with brood sizes ranging from two to five. A greater percentage of families in an 1100-nest colony had non-kin offspring than in two smaller colonics, although the difference was not statistically significant. Application of genetic models to these data and the observed distribution of parental exclusions suggested that multiple parentage in cliff swallows results more often from intraspecific brood parasitism than from forced extra-pair copulations. Based on the calculated probabilities of detecting non-kin, we estimate that 23.7% of all nestlings in our population are not the offspring of one or both of their putative parents. We estimate that about 43% of all cliff swallow nests in Nebraska contain at least one offspring resulting from intraspecific brood parasitism, and that about 6% of nests might contain offspring resulting from extra-pair copulations.